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Aldersey JE, Lange MD, Beck BH, Abernathy JW. Single-nuclei transcriptome analysis of channel catfish spleen provides insight into the immunome of an aquaculture-relevant species. PLoS One 2024; 19:e0309397. [PMID: 39325796 PMCID: PMC11426453 DOI: 10.1371/journal.pone.0309397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 08/12/2024] [Indexed: 09/28/2024] Open
Abstract
The catfish industry is the largest sector of U.S. aquaculture production. Given its role in food production, the catfish immune response to industry-relevant pathogens has been extensively studied and has provided crucial information on innate and adaptive immune function during disease progression. To further examine the channel catfish immune system, we performed single-cell RNA sequencing on nuclei isolated from whole spleens, a major lymphoid organ in teleost fish. Libraries were prepared using the 10X Genomics Chromium X with the Next GEM Single Cell 3' reagents and sequenced on an Illumina sequencer. Each demultiplexed sample was aligned to the Coco_2.0 channel catfish reference assembly, filtered, and counted to generate feature-barcode matrices. From whole spleen samples, outputs were analyzed both individually and as an integrated dataset. The three splenic transcriptome libraries generated an average of 278,717,872 reads from a mean 8,157 cells. The integrated data included 19,613 cells, counts for 20,121 genes, with a median 665 genes/cell. Cluster analysis of all cells identified 17 clusters which were classified as erythroid, hematopoietic stem cells, B cells, T cells, myeloid cells, and endothelial cells. Subcluster analysis was carried out on the immune cell populations. Here, distinct subclusters such as immature B cells, mature B cells, plasma cells, γδ T cells, dendritic cells, and macrophages were further identified. Differential gene expression analyses allowed for the identification of the most highly expressed genes for each cluster and subcluster. This dataset is a rich cellular gene expression resource for investigation of the channel catfish and teleost splenic immunome.
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Affiliation(s)
- Johanna E. Aldersey
- Oak Ridge Institute for Science and Education, Agricultural Research Service Research Participation Program, Oak Ridge, TN, United States of America
- United States Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, AL, United States of America
| | - Miles D. Lange
- United States Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, AL, United States of America
| | - Benjamin H. Beck
- United States Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, AL, United States of America
| | - Jason W. Abernathy
- United States Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, AL, United States of America
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Zhao L, Wang H, Zhang Y, Shi Y, Zhou C, Yu M, Wang Y, Zhang L, Xu Z, Zhang Z, Gao L, Zhang J, Yang B, Huang H, Wang FS. Characteristics and functions of an atypical inflammation-associated GZMK +GZMB +CD8 + T subset in people living with HIV-1. Mol Immunol 2024; 173:40-52. [PMID: 39053388 DOI: 10.1016/j.molimm.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
HIV-1 chronically infects host CD4+ T lymphocytes and further affects a variety of immune cells, including CD8+ T cells. In our previous study, by analyzing unbiased high-dimensional single-cell RNA-seq data (scRNA-seq), we found that the frequency of GZMK+CD8+ T cells expressing granzyme K (GZMK) was increased in people living with HIV-1 (PLWHs). However, the phenotypic and functional characteristics of these cells in chronic HIV-1 infection and their correlation with disease are not well understood. In this study, we conducted a comprehensive analysis of scRNA-seq and matched T-cell receptor repertoire (TCR) sequencing data to delve into the characterizations of GZMK+CD8+ T cells, which was further validated by flow cytometry. We observed heterogeneity within the GZMK+CD8+ T cells, which could be further subdivided into a GZMK+GZMB- subset and a GZMK+GZMB+ subset, with the latter being significantly enriched in PLWHs. The GZMK+GZMB+ cells are a unique subset within CD8+ T cells, characterized by high proliferation, activation, inflammatory response, clone transition, etc., and are one of the differentiation endpoints by pseudotemporal analysis of CD8+αβ T cells. Despite being predominantly composed of effector memory T cells (Tem), similar to the GZMK+GZMB- subset, the GZMK+GZMB+ subset exhibits differentiation at a later stage than the GZMK+GZMB- subset. We also observed that the frequency/count of GZMK+GZMB+CD8+ T cells was negatively correlated with CD4/CD8 ratio, and positively correlated with HIV DNA, IP-10, and MIG levels in PLWHs. In vitro experiments demonstrate that GZMK can potentiate the stimulatory effects of lipopolysaccharide (LPS) on THP-1 macrophages via the TLR-4 pathway, significantly enhancing the secretion of IP-10, MIG, and MCP-1, as well as increasing the proportion of TNF-α+ cells. In conclusion, in PLWHs, GZMK+GZMB+CD8+ T cells are a highly reactive and inflammatory-inducing subset that may be associated with systemic inflammation.
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Affiliation(s)
- Liang Zhao
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Huifang Wang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Senior Department of Infectious Diseases and Hepatology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanze Shi
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chunbao Zhou
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Minrui Yu
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanhu Wang
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Liping Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zheng Xu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Xinjiang, China
| | - Ziying Zhang
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lingyu Gao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jiyuan Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Baopeng Yang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Huihuang Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Fu-Sheng Wang
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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Qiu S, Lin W, Zhou Z, Hong Q, Chen S, Li J, Zhong F, Zhou Q, Cui D. TOX: a potential new immune checkpoint in cancers by pancancer analysis. Discov Oncol 2024; 15:354. [PMID: 39152366 PMCID: PMC11329495 DOI: 10.1007/s12672-024-01236-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Thymocyte selection-associated HMG-BOX (TOX) belongs to a family of transcription factors containing a highly conserved region of the high mobility group box (HMG-Box). A growing body of research has shown that TOX is involved in the occurrence and development of tumors and promotes T-cell exhaustion. We assessed the role of TOX with The Cancer Genome Atlas (TCGA) Pancancer Data. METHODS TOX expression was examined with RNA-seq data from the TCGA and Genotype-Tissue Expression (GTEx) databases. The genetic alteration status and protein level of TOX were analyzed using databases, including the Human Protein Atlas (HPA), GeneCards, and STRING. The prognostic significance was estimated with survival data from the TCGA. Moreover, R software was used for enrichment analysis of TOX. The relationship between TOX and immune cell infiltration was assessed with the Tumor Immune Estimation Resource (TIMER) 2.0 database and the "CIBERSORT" method. The correlation between TOX and immune checkpoints was further explored. Immunohistochemical analysis was used to further verify the difference in TOX expression between cancerous and paracancerous tissues, and cell viability was evaluated using a CCK-8 assay. RESULTS In most cancer types in the TCGA cohort, differential TOX expression was observed. The genetic alteration status and protein level of TOX were examined, and the prognosis of cancers was associated with TOX expression. Moreover, TOX levels were closely related to different immune-related pathways, immune cell infiltration and immune checkpoints. Additionally, significant differences in TOX expression between several cancerous and paracancerous tissues were validated. Furthermore, TOX clearly impacted the viability of cancer cells. CONCLUSIONS TOX, a potential biomarker for cancer, may be involved in the regulation of the immune microenvironment and can be used for new targeted drugs.
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Affiliation(s)
- Shengliang Qiu
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), 54 Youdian Road, Hangzhou, 310006, China
| | - Weiye Lin
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, 310053, China
| | - Zhengyang Zhou
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, China
| | - Qianran Hong
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, 310053, China
| | - Shuangyu Chen
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, 310053, China
| | - Jiayang Li
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, 310053, China
| | - Fengyun Zhong
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004, China.
| | - Qinfeng Zhou
- Department of Laboratory Medicine, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, 4 Kangle Road, Zhangjiagang, 215600, China.
| | - Dawei Cui
- The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China.
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Zeng M, Zhou T, Li Z, Li G, Zhang S, Wang L, Huang Q, Li J, Samarawickrama PN, He Y, Wang G. Transcriptomic and intervention evidence reveals domestic dogs as a promising model for anti-inflammatory investigation. Aging Cell 2024; 23:e14127. [PMID: 38426629 PMCID: PMC11113267 DOI: 10.1111/acel.14127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 03/02/2024] Open
Abstract
Domestic dogs have great potential to expand our understanding of the determinants of aging. To understand the aging pattern of domestic dogs and evaluate whether they can be used as an aging model, we performed RNA sequencing on white blood cells from domestic dogs aged 1-9 years and treated aged dogs with classical antiaging approaches. We obtained 30 RNA sequencing libraries and identified 61 age-associated genes with dynamic changes, the majority of which were related to metabolism and immune function, which may be predominant biomarkers for aging in dogs. We next treated aged dogs with canine mesenchymal stem cells (cMSCs), nicotinamide mononucleotide, and rapamycin to determine whether and how they responded to the antiaging interventions. The results showed that these treatments can significantly reduce the level of inflammatory factors (IL-6 and TNF-α). MSCs effectively improved the heart functions of aged dogs. Three key potential age-related genes (PYCR1, CCRL2, and TOX) were reversed by MSC treatment, two of which (CCRL2 and TOX) are implicated in immunity. Overall, we profiled the transcriptomic pattern of domestic dogs and revealed that they may be a good model of aging, especially in anti-inflammatory investigations.
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Affiliation(s)
- Min Zeng
- Key Laboratory of Genetic Evolution & Animal ModelsKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina
| | - Tong Zhou
- Key Laboratory of Genetic Evolution & Animal ModelsKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Zhiyu Li
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in YunnanYunnan UniversityKunmingChina
| | - Guimei Li
- Key Laboratory of Genetic Evolution & Animal ModelsKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Shurun Zhang
- Key Laboratory of Genetic Evolution & Animal ModelsKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in YunnanYunnan UniversityKunmingChina
| | - Qing‐Guo Huang
- Kunming Police Dog Base of the Chinese Ministry of Public SecurityKunmingChina
| | - Ju‐Dong Li
- Kunming Police Dog Base of the Chinese Ministry of Public SecurityKunmingChina
| | - P. Nadeeshika Samarawickrama
- Key Laboratory of Genetic Evolution & Animal ModelsKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina
- Key Laboratory of Healthy Aging Research of Yunnan ProvinceChinese Academy of SciencesKunmingChina
| | - Yonghan He
- Key Laboratory of Genetic Evolution & Animal ModelsKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina
- Key Laboratory of Healthy Aging Research of Yunnan ProvinceChinese Academy of SciencesKunmingChina
| | - Guo‐Dong Wang
- Key Laboratory of Genetic Evolution & Animal ModelsKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Molecular Biology of Domestic AnimalsChinese Academy of SciencesKunmingChina
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Burg MML, Visser L, Diepstra A. TOX as a new diagnostic marker for T cell large granular lymphocytic leukaemia. Histopathology 2024; 84:697-701. [PMID: 38087646 DOI: 10.1111/his.15114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/10/2023] [Accepted: 11/25/2023] [Indexed: 02/07/2024]
Abstract
AIMS T cell large granular lymphocytic leukaemia (T-LGLL) is a rare disorder that may underlie otherwise unexplained cytopenias. The identification of T-LGLL cells in bone marrow biopsies can be a challenge, because a robust immunohistochemistry marker is lacking. The markers currently in use (granzyme B, TIA-1 and CD8) are difficult to interpret or lack specificity. Therefore, we investigated whether immunohistochemistry for thymocyte selection-associated high-mobility group box (TOX), a transcription factor that associates with chronic T cell stimulation, could be a reliable tool for the identification of T-LGLL cells. METHODS AND RESULTS In this retrospective study, expression of TOX in CD8+ cells in bone marrow biopsies of T-LGLL patients (n = 38) was investigated and compared to bone marrow of controls with reactive T cell lymphocytosis (n = 10). All biopsies were evaluated for TOX staining within the CD8-positive T cell population. The controls were essentially negative for TOX, whereas all T-LGLL cases were positive (median = 80%, range = 10-100%), even when bone marrow involvement was subtle. CONCLUSION TOX is a highly sensitive marker for the neoplastic cells of T-LGLL and we recommend its use, especially in the diagnostic work-up of patients with unexplained cytopenias.
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Affiliation(s)
- Manske M L Burg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Lydia Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
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Kogame T, Egawa G, Nomura T, Kabashima K. Waves of layered immunity over innate lymphoid cells. Front Immunol 2022; 13:957711. [PMID: 36268032 PMCID: PMC9578251 DOI: 10.3389/fimmu.2022.957711] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Innate lymphoid cells (ILCs) harbor tissue-resident properties in border zones, such as the mucosal membranes and the skin. ILCs exert a wide range of biological functions, including inflammatory response, maintenance of tissue homeostasis, and metabolism. Since its discovery, tremendous effort has been made to clarify the nature of ILCs, and scientific progress revealed that progenitor cells of ILC can produce ILC subsets that are functionally reminiscent of T-cell subsets such as Th1, Th2, and Th17. Thus, now it comes to the notion that ILC progenitors are considered an innate version of naïve T cells. Another important discovery was that ILC progenitors in the different tissues undergo different modes of differentiation pathways. Furthermore, during the embryonic phase, progenitor cells in different developmental chronologies give rise to the unique spectra of immune cells and cause a wave to replenish the immune cells in tissues. This observation leads to the concept of layered immunity, which explains the ontology of some cell populations, such as B-1a cells, γδ T cells, and tissue-resident macrophages. Thus, recent reports in ILC biology posed a possibility that the concept of layered immunity might disentangle the complexity of ILC heterogeneity. In this review, we compare ILC ontogeny in the bone marrow with those of embryonic tissues, such as the fetal liver and embryonic thymus, to disentangle ILC heterogeneity in light of layered immunity.
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